rs1808089

Positions:

• chr8-75308421-A-G
• chr8-75308421-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000676364.1(CASC9):​n.250+15800T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,976 control chromosomes in the GnomAD database, including 18,724 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18724 hom., cov: 32)
• Consequence: CASC9 ENST00000676364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

CASC9 (HGNC:48906): (cancer susceptibility 9)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC9	ENST00000676364.1	n.250+15800T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74582 AN: 151856 Hom.: 18721 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.500

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.491 AC: 74607 AN: 151976 Hom.: 18724 Cov.: 32 AF XY: 0.492 AC XY: 36567 AN XY: 74294

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.496

Alfa AF: 0.518 Hom.: 3559

Bravo AF: 0.497

Asia WGS AF: 0.398 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1808089; hg19: chr8-76220656;